Kegg glycan is a publicly accessible database where a unique structure corresponds to an entry annotated with various information for the structure, including composition, class. They are the variable portions of nglycans, oglycans, and glycolipids that are attached to the core sugars characteristic of each glycan class. The glycanbuilder has been developed for the eurocarbdb project with the purpose of creating a fast, intuitive and flexible software tool for building and displaying glycan structures. Includes a database of over 22500 glycans to process and verify structures. Consequently, we have built a relational database glycobase and an analytical tool autogu in conjunction with. Simglycan software for automated glycan structural elucidation. Customizable glycan structure database profile database manager. The importance of the eurocarbdb initiative in the development of glycan structure databases has been widely recognized 1, 2.
Users can load tandem ms data to obtain glycan structure and linkage information. Olinked glycosylation is a true posttranslational event and does not require a consensus sequence. It also provides a userfriendly interface to draw glycan structures which can then be used to annotate the mass spectrum. Type glycan or glycopeptide string in standard iupaccondensed nomenclature see examples 2.
The open source software glycoworkbench developed within the eurocarb project to assist manual annotation of msms data 68 can be used to record glycan structures. These glcnac sequences added to the nlinked glycan core in hybrid and complex nglycans are called antennae. More relevant information about the proposed structure, including the glycan. Source code, standalone version and packages compiled in java and python supporting. However the interpretation, annotation and assignment of hplcglycan data is currently a manual and very timeconsuming aspect of glycan analysis performed by experts anumula, 2000. Simglycan provides for every probable glycan result, the glycan fragments, structure, sequence, composition, glycan mass, class, reaction, pathway, enzyme and other database links, allowing easy access to all published glycan information without referring to multiple sources. Instructions this software implements the symbol nomenclature for glycans snfg. Charmm, namd, gromacs, amber, genesis, lammps, desmond, and openmm.
Manual interpretation of exoglycosidase data is complex and time consuming. Glycamweb utilities for molecular modeling of carbohydrates. Sbio offers a line of cell culture labware with demonstrated high performance for glycan analysis. Answer the question which nglycans are in my product and at what level. Because manual interpretation of exoglycosidase data is complex and. Discrimination of isomers of released n and o glycans. Glycosylation manual biological small angle scattering. Highthroughput automated micropermethylation for glycan.
The lower structure is a triantennary glycan with three glcnac branches. Glycoworkbench is a software tool developed by the eurocarbdb initiative to assist the manual interpretation of ms data. Perform released nglycan analysis and characterization by liquid chromatography lc and lcms. Glycanmass is a tool which allows to calculate the mass of an oligosaccharide structure mass values disclaimer note. You can use glycomod to predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. Simglycan predicts structure of glycans from the msms and multistage mass spectrometry ms n data. Glycananalyzer significantly improves assignment accuracy over other autoassignment methods on tests. Structures common to different glycans essentials of.
Perform glycan and glycopeptide qualitative analysis, glycan structure. The lower antenna ends with a galactose and thus the second position of the abbreviation is an a leading to gna. N and olinked glycans from the same protein can be. Glycoworkbench is a software tool that contains features for structure drawing, assignment of glycan compositions from mass spectra, and assignment of product ions from tandem mass spectra. For peak labeling, both the nomenclature used in various publications4, 5, 10 and the nomenclature of the agilent mabglyco chip manual was used. The software allows not just to load, visualize and browser glycomics ms data but also to annotate the data with glycan structures and their fragments. The glycan structure on this glycosylation site plays a critical role in complement activation and receptor af. Determination of glycan structures from analysis of ms data is a major bottleneck in highthroughput glycomics projects, and robust solutions to this problem are of. Here, we focus on the glycan profiling functionality of the software from a single ms spectrum prospect. Simglycan software for automated glycan structural elucidation author. Utilize comprehensive capabilities for the analysis of nlinked glycosylation.
A user friendly inputoutput tool for glycan structures should provide an intuitive interface to build. Stores a collection of experimentally determined glycan structures. Instructions this software implements the symbol nomenclature for glycans. Nglycan analysis of monoclonal antibodies and other.
Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Glycananalyzer is a web application that pattern matches nglycan peak shifts following exoglycosidase digestion and automates structure assignments. Automatic annotated data can be manually evaluated, changed and exported to excel. Each entry contains monosaccharide composition, linkage information, amino acid sequence if glycopeptide and the. Assign an unequivocal glycan structure to every glycoform by performing glycan release and carbohydrate substructural analysis. Provides a wealth of relevant biological information for the probable glycan structure, including glycan class, reaction, pathway, and. The most common type of olinked glycans contain an initial galnac residue or tn epitope. This tool detects and quantifies any likely errors in a glycan 3d structure.
Simglycan software for glyco analysis 103841001 sciex. Because manual interpretation of exoglycosidase data is complex and time consuming, we developed glycananalyzer, a web application that pattern matches nglycan peak shifts following. This presentation describes the challenges of glycomics and the utility of liquid chromatography mass spectrometry and simglycan software for the elucidation of. A new predictive carbohydrate analysis tool for msms data. While several software solutions exist for semiautomated glycan spectral annotation from liquid. Highthroughput automated micropermethylation for glycan structure analysis asif shajahan, nitin supekar, christian heiss, and parastoo azadi complex carbohydrate research center, the university of georgia, athens, georgia 30602, united states. Glycoworkbench is a software tool that contains features for structure.
The sequon is an asnxser or asnxthr sequence, where x is any amino acid except proline and the glycan may be composed of nacetylgalactosamine, galactose, neuraminic acid, nacetylglucosamine, fucose, mannose, and other monosaccharides. Novel automated and manual nglycan sample preparation. Software tools for glycan profiling pubmed central pmc. Nlinked glycosylation, is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom the amide nitrogen of an asparagine asn residue of a protein, in a process called nglycosylation, studied in biochemistry. This type of linkage is important for both the structure and function of some eukaryotic.
You can view the glycan structure in the glycan structure. Glycan functions are often dependent on the structure of the oligosaccharide. Simglycan software automatically matches the experimentally acquired mass spectra against its database of theoretical glycan fragments, and generates a list of candidate glycan structures. Such microarrays, though still relatively limited in complexity and diversity of glycans, have made profound impacts on a number of fields of study, including immunology. This is the manual for glycosylation, a program to be used in conjunction with sasref for rigid body modeling of glycosylated structures. Moreover, nonhuman glycans represent a safety issue due to induced immune responses. Nlinked glycans are attached in the endoplasmic reticulum to the nitrogen n in the side chain of asparagine in the sequon. Grits toolbox is a glycomics ms data processing software. Olinked glycans are usually attached to the peptide chain through serine or threonine residues. Manual analysis of the glycan profiling lcms data is extremely. Exoglycosidase cleavage of monosaccharides results in signature peak shifts, in both uplc and ms1.
Simglycan software predicts the structure of a glycan from the msms data. This tool predicts nmr scalar jcouplings and noe intensities and interproton distances for a given glycan structure. Key features of simglycan software imports experimental msms data generated by all ab. Therefore, analysis of the glycan pattern is an important part. Speed the characterization of complex glycans using simglycan software from. The core structures of nglycans, oglycans, and glycolipids figure.
Glycan may also refer to carbohydrate portions of glycoprotein, glycolipid, or a proteoglycan. Because manual interpretation of exoglycosidase data is complex and time consuming, we developed glycananalyzer, a web application that pattern matches nglycan peak shifts following exoglycosidase digestion and automates structure assignments. Software for automated interpretation of mass spectrometry data. Glycan and glycopeptide analysis mass spectra interpretation. This chapter describes terminal glycan structures that are common to different classes of glycans.
The input is a glycan mass list and the program is not applicable to automated data analysis of lcms datasets. The uppermost structure shown in figure 3 is a biantennary glycan with two glcnac branches linked to the core. Simglycan software a product of premier biosoft predicts glycan and glycopeptide structures from sciex mass spectrometeracquired msms data, facilitating the identification of glycosylation sites and posttranslational modifications. Glycan microarrays afford an unprecedented opportunity to explore a wide range of glycan recognition by gbps, cells, and even organisms. Towards a standardized bioinformatics infrastructure for n. Manual annotation of fragment spectra comprises a series of. Most software for glycan modeling on a personal desktop computer requires. The graphical interface of glycoworkbench provides an environment in which structure models can be rapidly assembled, their masses can be computed, their fragments. Software for automated interpretation of mass spectrometry. The glycanbuilder and glycoworkbench glycoinformatics tools. Glycanmodified proteins are involved in a wide range of biological and physiological processes including recognition and regulatory functions, cellular communication, gene expression, cellular immunity, growth, and development. Go to charmmgui input generator to read the pdb structure with glycans for various simulation programs. Users can either draw a specific structure or search certain glycans in public glycan database via glycoworkbench. Software can automatically assign glycan structures by matching their.
849 956 139 1217 1644 870 144 797 1601 607 1660 1487 1250 241 294 1646 668 725 691 693 1275 212 679 681 1269 390 1677 768 1126 1055 607 181 1040 1644 289 829 798 1490 1437 210 1063 333